The idea that an animal can be known without being seen has an almost poetic quality. In water so dark it could pass for space, a jellyfish floats by. It leaves no traces, no sound, and no shadow in its wake. Nevertheless, it has left a DNA trace of itself in the water itself. These traces are now being read by scientists, and what they discover is subtly altering our understanding of one of the planet’s least-known locations.
The genetic material that organisms shed as they move through their surroundings is known as environmental DNA, or eDNA as researchers refer to it. waste, tissue fragments, mucus, and scales. Things that don’t seem to matter. This biological residue, which is obtained from seawater samples that have been raised from depths greater than 200 meters, can be filtered, amplified, and compared to known genetic libraries to create a list of species that have lived in that water column, sometimes recently and sometimes not. Marine biologists seem to be still getting used to the fact that it’s more akin to forensics than fieldwork.
The first eDNA dataset collected aboard NOAA Ship Okeanos Explorer has now been made public by NOAA Ocean Exploration, in collaboration with the Ocean DNA Program of the Smithsonian National Museum of Natural History and NOAA’s Atlantic Oceanographic and Meteorological Laboratory. The information includes expeditions that took place in various parts of the Atlantic and Pacific between 2021 and 2023. Evidence of invertebrates, fish, marine mammals, corals, and microbes were among the discoveries; some species had been seen on previous dives, while others, such as the barreleye fish with its tubular eyes and translucent head, had never been visually confirmed in those areas.
Deep-sea exploration has required ROVs, nets, and hours of frame-by-frame video review by weary researchers for decades. The video is frequently breathtaking. It’s also lacking. Habitat is harmed by nets. The timid, small, and quick are missed by cameras. The deep ocean is vast, dark, and largely unaffected by schedules, and a remotely operated vehicle can only see what is directly in front of it. The scientific community has long been aware that visual surveys only capture a small portion of what is truly present.
This is where eDNA makes a difference, albeit not significantly, and scientists are cautious about overpromoting it. You cannot determine the precise time or number of people present from a water sample. It doesn’t demonstrate behavior. The visceral, humble experience of watching a giant squid on a live ROV feed cannot be replaced. It can fill in the background of a scene that was previously nearly completely empty, and it does this remarkably well. Some of the species that are currently showing up in these datasets may have been residing in those depths for centuries without ever being observed by humans.
The discoveries made possible by this logistical pipeline are more impressive than the pipeline itself. While the ship is still at sea, scientific teams on board the Okeanos Explorer use ROV equipment to gather water samples, filter the material in a wet lab, and preserve it for analysis back onshore. The DNA is then sequenced by the National Systematics Laboratory. Taxonomic identities are assigned by NOAA’s AOML team. The data eventually ends up in publicly accessible repositories, such as the Ocean Biodiversity Information System and the NCBI, where it can be downloaded and used by any researcher, anywhere. Open science is desperately needed in this field.
This feels very different from traditional expedition science, which has frequently been costly, time-consuming, and challenging to duplicate. Without destroying coral colonies, an eDNA sample from a single water column can provide information that would have required weeks of net trawling. Primnoa pacifica, the red tree coral seen on recent dives, is one example of a deep-sea coral that is infamously delicate and still poorly understood. Beyond scientific curiosity, it is important to be able to genetically detect their presence without physical contact. Commercially valuable fisheries are supported by these habitats. The economic impact of what we don’t know about them is significant.
It’s still unclear if eDNA will eventually be used in all significant oceanographic surveys. Large amounts of data are involved, analytical techniques are still being improved, and matching genetic sequences to known species only functions when those species have already been cataloged, which is far from certain in the deep ocean. However, something is obviously changing. The ocean has always maintained its own records. The ability to read them is a relatively new skill for scientists.
